The Kootenai River Resident Fish Mitigation project is comprised of several studies specifically focused on the recovery of white sturgeon (ESA listed), burbot, and salmonid fish populations in the Kootenai River. Over the past three decades, the Kootenai River has experienced many physicochemical changes, and as a result, native fish species have dramatically declined. Construction and operation of Libby Dam has changed the river ecosystem, particularly by altering the discharge and water temperature regimes. In addition, the reservoir behind the dam (Lake Koocanusa) effectively traps macro-nutrients. As a consequence of these physical and chemical changes, the Kootenai River has experienced reduced trophic level productivity, altered fish community structure (increased omnivore density), inadequate recruitment of white sturgeon and burbot, and reduced density of salmonid species. The overall goal of our project is to restore these native fish populations to the Kootenai River. These recovery investigations are trans-boundary in nature, and we closely collaborate with several state, federal, provincial, and tribal agencies to achieve common objectives. Our research is designed to identify strategies that will aid in reaching set recovery goals of focal species.

Our white sturgeon research is designed to integrate the Reasonable and Prudent Measures identified in the USFWS Biological Opinions to recover this species. Our sturgeon studies have provided information on spawning location, timing, and population vital statistics. This information has allowed mitigation strategies to be developed and has provided biological information that has been used to improve dam operations. There are a variety of key findings from our research. For instance, mitigated flows can improve spawning success; however, the primary spawning reach is unsuitable for egg incubation and larval rearing. Also, now the wild sturgeon population only produces about ten new recruits each year and population viability analysis (PVA) suggests that at least 200 recruits each year are necessary to recover the population in 25 years. Significant numbers of sturgeon move to river reaches near Bonners Ferry and spawn in what is considered more suitable substrate for incubation, and eggs collected in these locations survive longer into development. Additionally, recent hatchery sturgeon captures much further upstream in Montana indicate that some hatchery reared juvenile sturgeon do utilize this gravel and cobble habitat. To build on what we have learned, our upcoming proposal describes a plan to investigate why only a portion of these fish move to upstream reaches and if they are utilizing suitable spawning substrate. We will work directly with the ACOE and KTOI to provide the proper discharge, temperature, and physical habitat improvements needed to increase the number of sturgeon that use these suitable substrates.

Our burbot research has shown that winter discharge (>12 kcfs) may impair burbot movement rate, migration distance, and spawning success. In addition, warmer winter temperatures may have significant impacts on burbot egg hatching success. A PVA analysis was also performed on a hypothetical Kootenai burbot stock based on population statistics derived from modest density stocks elsewhere. This analysis resulted in Kootenai River burbot rehabilitation goals of 5,500 fish in the interim and an ultimate goal of 17,500 fish. With collaborative efforts from KTOI and BCMFLRNO, our burbot extensive rearing ponds have provided information on density dependent growth and overall survival of hatchery reared burbot larvae. Our upcoming proposal outlines investigations on all life-history stages. In response to current and anticipated hatchery stocking events, we will be expanding our evaluation to determine stocking effects on burbot survival and natural production. In addition, these stockings will provide a unique opportunity to better understand burbot early-life-history and aid us in developing future ecosystem management actions with partner agencies. The proposed research will also evaluate how recent changes in winter discharge and temperature resulting from Libby Dam operations will affect burbot spawning.

Through our salmonid and ecosystem restoration studies we have worked cooperatively with the Kootenai Tribe of Idaho (KTOI) to evaluate the effects of nutrient additions to the entire Kootenai River fish community. Addition of nutrients from 2005-2010 has resulted in improved productivity across trophic levels. To date, we have seen significant increases in chlorophyll a, periphyton, and macroinvertebrates (Holderman and Gidley eds 2011). Since nutrient additions began, total electrofishing catch rates increased substantially in response to treatments. Overall catch per unit effort (CPUE) for fish (fish/hr) increased significantly at treatment reach sites (KR6 and KR9) post nutrient addition (Gidley in progress). CPUE has more than doubled at site KR9 from 276 to 607 fish/hr (F=5.94, P=0.018) and increased from 300 to 558 fish/hr at site KR6 (F=7.59, P=0.008). Fish condition (Wr and K) increased for rainbow trout post nutrient addition, and mountain whitefish have shown improvement in both Wr and growth, for age-0 and age-1 year classes. Since the nutrient additions, mountain whitefish abundance in our trend evaluation reach increased 2.5 fold and rainbow trout increased 1.7 fold. Recent mountain whitefish population estimates are similar to the abundance reported in 1980-1981, which is considered to reflect “pre-dam “conditions. These data demonstrate that nutrient addition sustains higher fish densities in the Kootenai River above Bonners Ferry. Through our salmonid studies, we have determined that rainbow trout recruitment is low, and a large proportion of rainbow trout adults spawn in Montana tributaries. To improve recruitment, we have recently conducted habitat improvements to Deep Creek tributaries that will improve rainbow trout access to historical spawning sites. Our proposed work with respect to ecosystem and salmonid studies will involve continued cooperative efforts to add nutrients to the Kootenai River to improve the general fish community. In addition, we will identify on the ground mitigation work that may directly improve rainbow trout recruitment from Idaho tributaries.